I have installed both as well and agree with Michael.
One advantage (particularly if you are using a donor wiring harness) is the smaller size of the later model pedal boxes. You will appreciate the extra room when you start stuffing this area full of your wiring bundle.
94 and up are much easier to package into the foot box due to their size. If you want to use late model Bullitt pedal pads or aftermarket, they fit the '94 and up better. If you plan on using hydroboost then the '94 and up is also the better option (actually '96 and up GT/Cobra)...
We used a '96 GT pedal box for our build with hydroboost and everything fit like a glove...
Don't feel bad as I, and most everyone of us have, ON RARE OCCAYSIONS, also made a MISTAKE (or two, or three, or four, or oh well you get my point). It's just a small part of one of the BEST GROUPS you'll EVER ba part of !!!
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